Pop star Elton John and partner David Furnish were joined in a civil partnership in 2005. A law change means gay couples can now hold partnership ceremonies in places of worship. Photograph: Graeme Robertson

The Church of England has announced that it will not allow civil partnership ceremonies to take place in its churches unless the full General Synod gives its consent.

A law enabling same-sex couples to register their partnerships in places of worship, removing a key legal distinction between the ceremony and marriage, comes into force on Monday.

But in a letter to the synod, secretary general William Fittall said no Church of England religious premises could host the registration of partnerships without written permission from the national assembly.

Peter Tatchell, the gay rights campaigner, called the move an "infringement of religious freedom" and criticised the government for failing to force religious groups to host the ceremonies.

But the church's legal office said its regulations do not constitute unlawful discrimination under the Equality Act as marriage and civil partnerships are different services and legally distinct concepts.

It said in a statement: "A gentlemen's outfitter is not required to supply women's clothes. A children's bookshop is not required to stock books that are intended for adults.

"And a church that provides a facility to marry is not required to provide a facility to same-sex couples for registering civil partnerships."